Fig. 2: The putEC structure.

a The cryo-EM map of the putEC (3.2 Å-resolution) is rendered as semi-transparent surface, colored as labeled, and superimposed with the putEC model. The RNAP domain that binds to putRNA, β‘ZBD, is highlighted in magenta. The putRNA boxed in red is re-drawn in cartoon format and colored from blue to red according to the residue numbers. b The putRNA is drawn in an orientation revealing its overall structure more clearly. The putRNA figure contains 73 nucleotides from U2* to U74* (the first and the last base-pairing residues are A3* and C72*, respectively), and has ‘V’-shape with two long stem-loop structures. The first stem region forms an RNA triplex. c A schematic diagram of the putRNA structure and its potential interactions with RNAP β’ and β subunits. The putRNA bases forming canonical WC base pairs and the unpaired bases are colored in light green. The bases forming non-canonical base pairs are colored in light purple. The RNA triplex region is marked in gray color, and the bases in the triplex are colored in orange. The pink and blue boxes represent β’ and β residues, respectively, and the lines between the RNAP residues and the putRNA nucleotides indicate potential hydrogen bond or salt bridge interactions. The ribose, shown as pentagon, and the phosphates, shown as circles, are colored in gray and the residue numbers of the putRNA are written in the ribose. Transcription bubble is marked with blue shade. d (Left) The predicted putRNA structure¹¹. The pausing site and the put⁻ mutation that abolishes the anti-termination activity are marked. Non-canonical base pairs are represented with red dotted line. (Right) The putRNA structure modeled based on the cryo-EM map. Triple helix region is marked by a gray box. Non-canonical base pairs are represented with red dotted lines. Transcription bubble region and the pausing site are marked.